Bobby Hassell's 35th-minute strike for a determined Tykes side inflicted a second successive defeat on the Hornets and left them nine points behind Championship leaders Cardiff in third place.
Zola said: "I'm disappointed for the result, I'm disappointed for the performance and that's it.
"But it ends there because sometimes you have to admit, when the opposition fights and plays the way they played, sometimes the better quality doesn't prevail - especially in the Championship when you have teams fighting for their lives, like Barnsley, and they make it difficult for you to play and you cannot overcome that.
"I think my players will learn a lot from today. For many of them, they didn't even know a game like this.
"It is the first time we have faced a team that has played and pressed us so much throughout the game.
"And as I said, many of them with learn. In my team I have a lot of young players and games like this will teach them a lot."